Neisseria meningitidis isolates are serotyped based on reaction with standardized sera representing immunological differences in Class 2 or Class 3 outer membrane proteins Sequences of genes for these proteins have revealed regions of variability between serotypes. We seek to develop a nonisotopic method of identifying N. meningitidis serotypes using DNA probes. Oligonucleotide probes to three variable regions (VR1,VR2,VR3) of two clinically significant serotypes (4 and 15) were synthesized and labeled with digoxigenin or biotin. Dot blots of genomic DNA from 27 strains of N. meningitidis were hybridized with each of the 6 probes. The VR1, VR2, and VR3 probes for serotype 15 were specific and identified all serotype 15 strains tested. We have found strain variation among serotype 4 isolates at the VR2 region. There is significant cross reaction of 5 other serotypes with the type 4 VR3 probe suggesting sequence similarities at these regions. We have cloned the class 3 protein genes from these serotypes (types 3, 8, 14, 17, 18) as well as a serotype 4 Brazilian strain BB 1350 for sequence analysis determination. We have analyzed these sequences along with sequences for other class 3 containing serotypes available through Gene Bank using a multiple sequence alignment program. We have demonstrated a method of identifying type 15 of N. meningitidis using nonisotopic DNA hybridization. We have expanded the available sequence data available for class 3 proteins to include all class 3 containing serotypes and are investigating variable regions of these serotypes to expand this methodology of serotype identification.